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Somatic inflammatory gene mutations in human ulcerative colitis epithelium 期刊论文
NATURE, 2020, 577 (7789) : 254-+
作者:  Nanki, Kosaku;  Fujii, Masayuki;  Shimokawa, Mariko;  Matano, Mami;  Nishikori, Shingo;  Date, Shoichi;  Takano, Ai;  Toshimitsu, Kohta;  Ohta, Yuki;  Takahashi, Sirirat;  Sugimoto, Shinya;  Ishimaru, Kazuhiro;  Kawasaki, Kenta;  Nagai, Yoko;  Ishii, Ryota;  Yoshida, Kosuke;  Sasaki, Nobuo;  Hibi, Toshifumi;  Ishihara, Soichiro;  Kanai, Takanori;  Sato, Toshiro
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

With ageing, normal human tissues experience an expansion of somatic clones that carry cancer mutations(1-7). However, whether such clonal expansion exists in the non-neoplastic intestine remains unknown. Here, using whole-exome sequencing data from 76 clonal human colon organoids, we identify a unique pattern of somatic mutagenesis in the inflamed epithelium of patients with ulcerative colitis. The affected epithelium accumulates somatic mutations in multiple genes that are related to IL-17 signalling-including NFKBIZ, ZC3H12A and PIGR, which are genes that are rarely affected in colon cancer. Targeted sequencing validates the pervasive spread of mutations that are related to IL-17 signalling. Unbiased CRISPR-based knockout screening in colon organoids reveals that the mutations confer resistance to the proapoptotic response that is induced by IL-17A. Some of these genetic mutations are known to exacerbate experimental colitis in mice(8-11), and somatic mutagenesis in human colon epithelium may be causally linked to the inflammatory process. Our findings highlight a genetic landscape that adapts to a hostile microenvironment, and demonstrate its potential contribution to the pathogenesis of ulcerative colitis.


  
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping 期刊论文
NATURE, 2020, 583 (7817) : 638-+
作者:  Lin, Yiheng;  Leibrandt, David R.;  Leibfriedz, Dietrich;  Chou, Chin-wen
收藏  |  浏览/下载:42/0  |  提交时间:2020/07/03

A method termed ac(4)C-seq is introduced for the transcriptome-wide mapping of the RNA modificationN(4)-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.


N-4-acetylcytidine (ac(4)C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA(1-3). However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac(4)C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac(4)C at single-nucleotide resolution. In human and yeast mRNAs, ac(4)C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac(4)C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. (AcC)-C-4 is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac(4)C and its potential thermoadaptive role. Our studies quantitatively define the ac(4)C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease(4-6).


  
Quantum crystal structure in the 250-kelvin superconducting lanthanum hydride 期刊论文
NATURE, 2020, 578 (7793) : 66-+
作者:  Gate, David;  Saligrama, Naresha;  Leventhal, Olivia;  Yang, Andrew C.;  Unger, Michael S.;  Middeldorp, Jinte;  Chen, Kelly;  Lehallier, Benoit;  Channappa, Divya;  De Los Santos, Mark B.;  McBride, Alisha;  Pluvinage, John;  Elahi, Fanny;  Tam, Grace Kyin-Ye;  Kim, Yongha;  Greicius, Michael;  Wagner, Anthony D.;  Aigner, Ludwig;  Galasko, Douglas R.;  Davis, Mark M.;  Wyss-Coray, Tony
收藏  |  浏览/下载:33/0  |  提交时间:2020/07/03

The discovery of superconductivity at 200 kelvin in the hydrogen sulfide system at high pressures(1) demonstrated the potential of hydrogen-rich materials as high-temperature superconductors. Recent theoretical predictions of rare-earth hydrides with hydrogen cages(2,3) and the subsequent synthesis of LaH10 with a superconducting critical temperature (T-c) of 250 kelvin(4,5) have placed these materials on the verge of achieving the long-standing goal of room-temperature superconductivity. Electrical and X-ray diffraction measurements have revealed a weakly pressure-dependent T-c for LaH10 between 137 and 218 gigapascals in a structure that has a face-centred cubic arrangement of lanthanum atoms(5). Here we show that quantum atomic fluctuations stabilize a highly symmetrical Fm (3) over barm crystal structure over this pressure range. The structure is consistent with experimental findings and has a very large electron-phonon coupling constant of 3.5. Although ab initio classical calculations predict that this Fm (3) over barm structure undergoes distortion at pressures below 230 gigapascals(2,3,) yielding a complex energy landscape, the inclusion of quantum effects suggests that it is the true ground-state structure. The agreement between the calculated and experimental Tc values further indicates that this phase is responsible for the superconductivity observed at 250 kelvin. The relevance of quantum fluctuations calls into question many of the crystal structure predictions that have been made for hydrides within a classical approach and that currently guide the experimental quest for room-temperature superconductivity(6-8). Furthermore, we find that quantum effects are crucial for the stabilization of solids with high electron-phonon coupling constants that could otherwise be destabilized by the large electron-phonon interaction(9), thus reducing the pressures required for their synthesis.


  
Prioritizing road defragmentation using graph-based tools 期刊论文
LANDSCAPE AND URBAN PLANNING, 2019, 192
作者:  Ascensao, Fernando;  Mestre, Frederico;  Marcia Barbosa, A.
收藏  |  浏览/下载:24/0  |  提交时间:2020/02/17
Carnivore conservation  Landscape connectivity  Linear infrastructures  Potential Biodiversity  Road mitigation  Spatial graphs  
Assessing landscape potential for human sustainability and 'attractiveness' across Asian Russia in a warmer 21st century 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2019, 14 (6)
作者:  Parfenova, Elena;  Tchebakova, Nadezhda;  Soja, Amber
收藏  |  浏览/下载:16/0  |  提交时间:2019/11/26
Ecological landscape potential  climate severity  permafrost  climate change  human population density  Asian Russia  
From intrinsic to service potential: An approach to assess tourism landscape potential 期刊论文
LANDSCAPE AND URBAN PLANNING, 2018, 170: 209-220
作者:  Wozniak, Edyta;  Kulczyk, Sylwia;  Derek, Marta
收藏  |  浏览/下载:5/0  |  提交时间:2019/04/09
Natural capacity  Cultural ecosystem services  Outdoor activities  Landscape planning  Analytic hierarchy process  Landscape potential  
Spatial transition analysis: Spatially explicit and evidence-based targets for sustainable energy transition at the local and regional scale 期刊论文
LANDSCAPE AND URBAN PLANNING, 2018, 169: 1-11
作者:  Oudes, Dirk;  Stremke, Sven
收藏  |  浏览/下载:6/0  |  提交时间:2019/04/09
Energy landscape  Stakeholder preferences  Energy potential maps  Energy-conscious  Landscape architecture  Landscape planning